1 740 236 CANCER/TESTIS ANTIGENS: EXPRESSION, REGULATION, TUMOR INVASION, AND USE IN IMMUNOTHERAPY OF CANCERS. CANCER/TESTIS ANTIGENS (CTAS) ARE NAMED BASED ON THEIR EXPRESSION PATTERN THAT IS RESTRICTED IN A NUMBER OF NORMAL AND ABNORMAL TISSUES. TUMOR CELLS FREQUENTLY EXPRESS ANTIGENS WHOSE EXPRESSION IS TYPICALLY RESTRICTED TO GERM CELLS. THEIR UNIQUE EXPRESSION PATTERN IS GUARANTEED BY PRECISE EPIGENETIC REGULATORY MECHANISMS. BECAUSE OF THEIR TUMOR-LIMITED, HIGH IMMUNOGENICITY, AND BIASED EXPRESSION, DISCOVERY OF THESE MOLECULES PROVIDES UNPRECEDENTED OPPORTUNITIES FOR FURTHER RESEARCH AND CLINICAL DEVELOPMENT IN THE FIELD OF CANCER DIAGNOSIS AND IMMUNOTHERAPY. EVOLVING EVIDENCE REVEALS THAT A NUMBER OF CTAS STIMULATE EPITHELIAL MESENCHYMAL TRANSITION (EMT) AND GENERATION OF CANCER STEM-LIKE CELLS, INTENSIFYING METASTASIS, INVASION, AND TUMORIGENESIS. BASED ON THESE FEATURES, CTAS ATTRACT ATTENTION TO BE CONSIDERED AS IDEAL TARGETS FOR DEVELOPING SEVERAL CLINICAL TRIALS, MANY OF THEM CONCENTRATING ON CTA VACCINE THERAPY. ACCORDING TO RECENT PRACTICAL CLINICAL INTEREST, MORE CHARACTERIZATIONS OF CTA REGULATION ARE IDENTIFIED. CTA EXPRESSION HAS BEEN DEMONSTRATED IN A VARIETY OF HUMAN CANCER TISSUES, AND SOME OF THEM HAVE BEEN FOUND TO ELICIT HUMORAL AND/OR CELLULAR IMMUNE RESPONSES IN CANCER PATIENTS. CTAS ARE BRILLIANT TARGETS FOR ANTICANCER DRUG DISCOVERY, TARGETED TUMOR THERAPY, AND DIAGNOSTIC BIOMARKERS, FURTHERMORE, VALUED GENES IN THE STUDY OF IMMUNOTHERAPY, PROMOTING TUMORIGENESIS, AND MALIGNANT PROGRESSION. THIS REVIEW OUTLINES AND CATEGORIZES OUR CURRENT UNDERSTANDING OF THE COMPLEX AND BIASED PROCESS OF CTAS MRNA AND PROTEIN EXPRESSION IN CANCER, AND SUPPLIES THE MOST RECENT INFORMATION ON THEIR REGULATION AND FUNCTION. BESIDES, A CONCISE SYNOPSIS OF THE MAJOR CLINICAL TRIALS INVOLVING CTAS, AS THERAPEUTIC AVENUES, IS DISCUSSED. ABBREVIATIONS: AIRE: AUTOIMMUNE REGULATOR; CAMP: CYCLIC ADENOSINE 3',5'-CYCLIC MONOPHOSPHATE; CEA: CARCINOEMBRYONIC ANTIGEN; CML: CHRONIC MYELOID LEUKEMIA; CREB: CYCLICAMP RESPONSE ELEMENT BINDING; CSCS: CANCER STEM CELLS; CTAS: CANCER/TESTIS ANTIGENS; CTL: CYTOTOXIC T LYMPHOCYTE; DCS: DENDRITIC CELLS; EMT: EPITHELIAL-MESENCHYMAL TRANSITION; ERK: EXTRACELLULAR SIGNAL-REGULATED KINASE; ESCC: ESOPHAGEAL SQUAMOUS CELL CARCINOMA; ETS: E26 TRANSFORMATION-SPECIFIC; HIS: HISTIDINE; HLA: HUMAN LEUKOCYTE ANTIGEN; HNSCC: HEAD AND NECK SQUAMOUS CELL CARCINOMA; IFN-GAMMA: INTERFERON-GAMMA; IHC: IMMUNOHISTOCHEMISTRY; IL-7: INTERLEUKIN7; MHC: MAJOR HISTOCOMPATIBILITY COMPLEX; MMP2: MATRIX METALLOPROTEINASE 2; MTECS: MEDULLARY THYMUS EPITHELIAL CELLS; MUC1: MUCIN 1; NSCLC: NON-SMALL CELL LUNG CANCER; PRAME: PREFERENTIALLY EXPRESSED ANTIGEN IN MELANOMA; RDA: REPRESENTATIONAL DIFFERENCE ANALYSIS; SEREX: SEROLOGICAL ANALYSIS OF CDNA EXPRESSION; SSX: SYNOVIAL SARCOMA X CHROMOSOME; TAAS: TUMOR-ASSOCIATED ANTIGENS; TCR: T-CELL RECEPTOR; TCGA: THE CANCER GENOME ATLAS; TGF-BETA: TRANSFORMING GROWTH FACTOR-BETA. 2016 2 3864 34 JAK-STAT PATHWAY INHIBITION PARTIALLY RESTORES INTESTINAL HOMEOSTASIS IN HDAC1- AND HDAC2-INTESTINAL EPITHELIAL CELL-DEFICIENT MICE. WE HAVE PREVIOUSLY REPORTED THAT HISTONE DEACETYLASE EPIGENETIC REGULATOR HDAC1 AND HDAC2 DELETION IN INTESTINAL EPITHELIAL CELLS (IEC) DISRUPTS MUCOSAL TISSUE ARCHITECTURE AND BARRIER, CAUSING CHRONIC INFLAMMATION. IN THIS STUDY, PROTEOME AND TRANSCRIPTOME ANALYSIS REVEALED THE IMPORTANCE OF SIGNALING PATHWAYS INDUCED UPON GENETIC IEC-HDAC1 AND HDAC2 DELETION. INDEED, GENE ONTOLOGY BIOLOGICAL PROCESS ANALYSIS OF ENRICHED DEFICIENT IEC RNA AND PROTEINS IDENTIFIED COMMON PATHWAYS, INCLUDING LIPID METABOLIC AND OXIDATION-REDUCTION PROCESS, CELL ADHESION, AND ANTIGEN PROCESSING AND PRESENTATION, RELATED TO IMMUNE RESPONSES, CORRELATING WITH DYSREGULATION OF MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) CLASS II GENES. TOP UPSTREAM REGULATORS INCLUDED REGULATORS ASSOCIATED WITH ENVIRONMENTAL SENSING PATHWAYS TO XENOBIOTICS, MICROBIAL AND DIET-DERIVED LIGANDS, AND ENDOGENOUS METABOLITES. PROTEOME ANALYSIS REVEALED MTOR SIGNALING IEC-SPECIFIC DEFECTS. IN ADDITION TO MTOR, THE STAT AND NOTCH PATHWAYS WERE DYSREGULATED SPECIFICALLY IN JEJUNAL IEC. TO DETERMINE THE IMPACT OF PATHWAY DYSREGULATION ON MUTANT JEJUNUM ALTERATIONS, WE TREATED MUTANT MICE WITH TOFACITINIB, A JAK INHIBITOR. TREATMENT WITH THE INHIBITOR PARTIALLY CORRECTED PROLIFERATION AND TIGHT JUNCTION DEFECTS, AS WELL AS NICHE STABILIZATION BY INCREASING PANETH CELL NUMBERS. THUS, IEC-SPECIFIC HISTONE DEACETYLASES 1 (HDAC1) AND 2 (HDAC2) SUPPORT INTESTINAL HOMEOSTASIS BY REGULATING SURVIVAL AND TRANSLATION PROCESSES, AS WELL AS DIFFERENTIATION AND METABOLIC PATHWAYS. HDAC1 AND HDAC2 MAY PLAY AN IMPORTANT ROLE IN THE REGULATION OF IEC-SPECIFIC INFLAMMATORY RESPONSES BY CONTROLLING, DIRECTLY OR INDIRECTLY, THE JAK/STAT PATHWAY. IEC-SPECIFIC JAK/STAT PATHWAY DEREGULATION MAY BE, AT LEAST IN PART, RESPONSIBLE FOR INTESTINAL HOMEOSTASIS DISRUPTION IN MUTANT MICE. 2021 3 5371 40 RECENT ADVANCES IN UNDERSTANDING THE GENETIC BASIS OF SYSTEMIC LUPUS ERYTHEMATOSUS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A POLYGENIC CHRONIC AUTOIMMUNE DISEASE LEADING TO MULTIPLE ORGAN DAMAGE. A LARGE HERITABILITY OF UP TO 66% IS ESTIMATED IN SLE, WITH ROUGHLY 180 REPORTED SUSCEPTIBILITY LOCI THAT HAVE BEEN IDENTIFIED MOSTLY BY GENOME-WIDE ASSOCIATION STUDIES (GWASS) AND ACCOUNT FOR APPROXIMATELY 30% OF GENETIC HERITABILITY. A VAST MAJORITY OF RISK VARIANTS RESIDE IN NON-CODING REGIONS, WHICH MAKES IT QUITE CHALLENGING TO INTERPRET THEIR FUNCTIONAL IMPLICATIONS IN THE SLE-AFFECTED IMMUNE SYSTEM, SUGGESTING THE IMPORTANCE OF UNDERSTANDING CELL TYPE-SPECIFIC EPIGENETIC REGULATION AROUND SLE GWAS VARIANTS. THE LATEST GENETIC STUDIES HAVE BEEN HIGHLY FRUITFUL AS SEVERAL DOZENS OF SLE LOCI WERE NEWLY DISCOVERED IN THE LAST FEW YEARS AND MANY LOCI HAVE COME TO BE UNDERSTOOD IN SYSTEMIC APPROACHES INTEGRATING GWAS SIGNALS WITH OTHER BIOLOGICAL RESOURCES. IN THIS REVIEW, WE SUMMARIZE SLE-ASSOCIATED GENETIC VARIANTS IN BOTH THE MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) AND NON-MHC LOCI, EXAMINING POLYGENETIC RISK SCORES FOR SLE AND THEIR ASSOCIATIONS WITH CLINICAL FEATURES. FINALLY, VARIANT-DRIVEN PATHOGENETIC FUNCTIONS UNDERLYING GENETIC ASSOCIATIONS ARE DESCRIBED, COUPLED WITH DISCUSSION ABOUT CHALLENGES AND FUTURE DIRECTIONS IN GENETIC STUDIES ON SLE. 2022 4 4962 50 PATHOGENESIS OF PSORIATIC ARTHRITIS. PSORIATIC ARTHRITIS (PSA) IS A CHRONIC INFLAMMATORY ARTHROPATHY INVOLVING SYNOVIAL AND ENTHESEAL STRUCTURES, ASSOCIATED WITH PSORIASIS OR SIMILAR CONDITIONS. THE ETIOPATHOGENETIC MECHANISMS UNDERLYING PSA REMAIN UNCLARIFIED. THE MOST ACCREDITED HYPOTHESIS INVOLVES A COMPLEX INTERACTION AMONG GENETIC, ENVIRONMENTAL, AND IMMUNOLOGICAL FACTORS. ENVIRONMENTAL AGENTS, PARTICULARLY TRAUMA, MECHANICAL STRESS, AND SMOKE HAVE BEEN CITED AS POSSIBLE FACTORS IN TRIGGERING THE DISEASE IN GENETICALLY PREDISPOSED SUBJECTS. LIKE OTHER FORMS OF SPONDYLOARTHROPATHIES, PSA SHOWS SEVERAL GENETIC ASSOCIATIONS WITH THE MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) CLASS I ALLELES LOCATED ON CHROMOSOME 6P21.3, PARTICULARLY THE HUMAN LEUKOCYTE ANTIGEN (HLA)-B27 IN AXIAL PHENOTYPES. RECENT STUDIES HAVE DEMONSTRATED THAT THE MOST COMMON EPIGENETIC MECHANISMS THAT REGULATE GENE EXPRESSION IN PSA ARE REPRESENTED BY DNA METHYLATION, PARENT OF ORIGIN EFFECT OR GENOMIC IMPRINTING, EXPRESSION OR ACTIVITY OF EPIGENETIC MODIFYING ENZYMES, AND RNA INTERFERENCE (RNAI) BY MICRORNAS (MIRNAS). THE MECHANISMS UNDERLYING PSA PATHOGENESIS ACTIVATE THE INNATE AND ADAPTIVE IMMUNE SYSTEM AND OVEREXPRESSION OF TNF ASSOCIATED WITH AMPLIFICATION OF THE IL-23/IL-17 AXIS. IN RECENT YEARS, MORE PSA SUSCEPTIBILITY GENES AND EPIGENETIC MECHANISMS HAVE BEEN IDENTIFIED. ADVANCES IN THE KNOWLEDGE OF INNATE AND ADAPTIVE IMMUNE MECHANISMS UNDERLYING PSA HAVE CONTRIBUTED TO A BETTER UNDERSTANDING OF THE HETEROGENEOUS CLINICAL EXPRESSION OF THE DISEASE AND, THUS, TO THERAPY STRATEGIES. THE COMPLEXITY OF THE PATHOGENETIC ASPECTS INVOLVING MULTIPLE CYTOKINES, CELL LINES, AND MOLECULES NEEDS TO BE FURTHER INVESTIGATED TO ADVANCE PERSONALIZED THERAPEUTIC STRATEGIES AND TO IMPROVE OUTCOMES OF PATIENTS AFFECTED BY PSA. 2019 5 2418 40 EPIGENETIC SIGNATURE OF CHRONIC LOW BACK PAIN IN HUMAN T CELLS. OBJECTIVE: DETERMINE IF CHRONIC LOW BACK PAIN (LBP) IS ASSOCIATED WITH DNA METHYLATION SIGNATURES IN HUMAN T CELLS THAT WILL REVEAL NOVEL MECHANISMS AND POTENTIAL THERAPEUTIC TARGETS AND EXPLORE THE FEASIBILITY OF EPIGENETIC DIAGNOSTIC MARKERS FOR PAIN-RELATED PATHOPHYSIOLOGY. METHODS: GENOME-WIDE DNA METHYLATION ANALYSIS OF 850,000 CPG SITES IN WOMEN AND MEN WITH CHRONIC LBP AND PAIN-FREE CONTROLS WAS PERFORMED. T CELLS WERE ISOLATED (DISCOVERY COHORT, N = 32) AND USED TO IDENTIFY DIFFERENTIALLY METHYLATED CPG SITES, AND GENE ONTOLOGIES AND MOLECULAR PATHWAYS WERE IDENTIFIED. A POLYGENIC DNA METHYLATION SCORE FOR LBP WAS GENERATED IN BOTH WOMEN AND MEN. VALIDATION WAS PERFORMED IN AN INDEPENDENT COHORT (VALIDATION COHORT, N = 63) OF CHRONIC LBP AND HEALTHY CONTROLS. RESULTS: ANALYSIS WITH THE DISCOVERY COHORT REVEALED A TOTAL OF 2,496 AND 419 DIFFERENTIALLY METHYLATED CPGS IN WOMEN AND MEN, RESPECTIVELY. IN WOMEN, MOST OF THESE SITES WERE HYPOMETHYLATED AND ENRICHED IN GENES WITH FUNCTIONS IN THE EXTRACELLULAR MATRIX, IN THE IMMUNE SYSTEM (IE, CYTOKINES), OR IN EPIGENETIC PROCESSES. IN MEN, A UNIQUE CHRONIC LBP DNA METHYLATION SIGNATURE WAS IDENTIFIED CHARACTERIZED BY SIGNIFICANT ENRICHMENT FOR GENES FROM THE MAJOR HISTOCOMPATIBILITY COMPLEX. SEX-SPECIFIC POLYGENIC DNA METHYLATION SCORES WERE GENERATED TO ESTIMATE THE PAIN STATUS OF EACH INDIVIDUAL AND CONFIRMED IN THE VALIDATION COHORT USING PYROSEQUENCING. CONCLUSION: THIS STUDY REVEALS SEX-SPECIFIC DNA METHYLATION SIGNATURES IN HUMAN T CELLS THAT DISCRIMINATES CHRONIC LBP PARTICIPANTS FROM HEALTHY CONTROLS. 2021 6 3056 30 GENOME-WIDE DNA METHYLATION ANALYSIS IMPLICATES ENRICHMENT OF INTERFERON PATHWAY IN AFRICAN AMERICAN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS AND EUROPEAN AMERICANS WITH LUPUS NEPHRITIS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC, MULTISYSTEM, INFLAMMATORY AUTOIMMUNE DISEASE THAT DISPROPORTIONATELY AFFECTS WOMEN. TRENDS IN SLE PREVALENCE AND CLINICAL COURSE DIFFER BY ANCESTRY, WITH THOSE OF AFRICAN AMERICAN ANCESTRY PRESENTING WITH MORE ACTIVE, SEVERE AND RAPIDLY PROGRESSIVE DISEASE THAN EUROPEAN AMERICANS. PREVIOUS RESEARCH ESTABLISHED ALTERED EPIGENETIC SIGNATURES IN SLE PATIENTS COMPARED TO CONTROLS. HOWEVER, THE CONTRIBUTION OF ABERRANT DNA METHYLATION (DNAM) TO THE RISK OF SLE BY ANCESTRY AND DIFFERENCES AMONG PATIENTS WITH SLE-ASSOCIATED LUPUS NEPHRITIS (LN) HAS NOT BEEN WELL DESCRIBED. WE EVALUATED THE DNA METHYLOMES OF 87 INDIVIDUALS INCLUDING 41 SLE PATIENTS, WITH AND WITHOUT LN, AND 46 CONTROLS ENROLLED IN AN ANCESTRY DIVERSE, WELL-CHARACTERIZED COHORT STUDY OF ESTABLISHED SLE (41 SLE PATIENTS [20 SLE-LN+, 21 SLE-LN-] AND 46 SEX-, RACE- AND AGE-MATCHED CONTROLS; 55% AFRICAN AMERICAN, 45% EUROPEAN AMERICAN). PARTICIPANTS WERE GENOTYPED USING THE INFINIUM GLOBAL DIVERSITY ARRAY (GDA), AND GENETIC ANCESTRY WAS ESTIMATED USING PRINCIPAL COMPONENTS. GENOME-WIDE DNA METHYLATION WAS INITIALLY MEASURED USING THE ILLUMINA METHYLATIONEPIC 850K BEADCHIP ARRAY FOLLOWED BY METHYLATION-SPECIFIC QPCR TO VALIDATE THE METHYLATION STATUS AT PUTATIVE LOCI. DIFFERENTIALLY METHYLATED POSITIONS (DMP) WERE IDENTIFIED USING A CASE-CONTROL APPROACH ADJUSTED FOR ANCESTRY. WE IDENTIFIED A TOTAL OF 51 DMPS IN CPGS AMONG SLE PATIENTS COMPARED TO CONTROLS. GENES PROXIMAL TO THESE CPGS WERE HIGHLY ENRICHED FOR INVOLVEMENT IN TYPE I INTERFERON SIGNALING. DMPS AMONG EUROPEAN AMERICAN SLE PATIENTS WITH LN WERE SIMILAR TO AFRICAN AMERICAN SLE PATIENTS WITH AND WITHOUT LN. OUR FINDINGS WERE VALIDATED USING AN ORTHOGONAL, METHYL-SPECIFIC PCR FOR THREE SLE-ASSOCIATED DMPS NEAR OR PROXIMAL TO MX1, USP18, AND IFITM1. OUR STUDY CONFIRMS PREVIOUS REPORTS THAT DMPS IN CPGS ASSOCIATED WITH SLE ARE ENRICHED IN TYPE I INTERFERON GENES. HOWEVER, WE SHOW THAT EUROPEAN AMERICAN SLE PATIENTS WITH LN HAVE SIMILAR DNAM PATTERNS TO AFRICAN AMERICAN SLE PATIENTS IRRESPECTIVE OF LN, SUGGESTING THAT ABERRANT DNAM ALTERS ACTIVITY OF TYPE I INTERFERON PATHWAY LEADING TO MORE SEVERE DISEASE INDEPENDENT OF ANCESTRY. 2023 7 1692 30 DURATION OF EXPOSURE TO EPIDURAL ANESTHESIA AT DELIVERY, DNA METHYLATION IN UMBILICAL CORD BLOOD AND THEIR ASSOCIATION WITH OFFSPRING ASTHMA IN NON-HISPANIC BLACK WOMEN. EPIDURAL ANESTHESIA IS AN EFFECTIVE PAIN RELIEF MODALITY, WIDELY USED FOR LABOR ANALGESIA. CHILDHOOD ASTHMA IS ONE OF THE COMMONEST CHRONIC MEDICAL ILLNESSES IN THE USA WHICH PLACES A SIGNIFICANT BURDEN ON THE HEALTH-CARE SYSTEM. WE RECENTLY DEMONSTRATED A NEGATIVE ASSOCIATION BETWEEN THE DURATION OF EPIDURAL ANESTHESIA AND THE DEVELOPMENT OF CHILDHOOD ASTHMA; HOWEVER, THE UNDERLYING MOLECULAR MECHANISMS STILL REMAIN UNCLEAR. IN THIS STUDY OF 127 MOTHER-CHILD PAIRS COMPRISED OF 75 NON-HISPANIC BLACK (NHB) AND 52 NON-HISPANIC WHITE (NHW) FROM THE NEWBORN EPIGENETIC STUDY, WE TESTED THE HYPOTHESIS THAT UMBILICAL CORD BLOOD DNA METHYLATION MEDIATES THE ASSOCIATION BETWEEN THE DURATION OF EXPOSURE TO EPIDURAL ANESTHESIA AT DELIVERY AND THE DEVELOPMENT OF CHILDHOOD ASTHMA AND WHETHER THIS DIFFERED BY RACE/ETHNICITY. IN THE MOTHER-CHILD PAIRS OF NHB ANCESTRY, THE DURATION OF EXPOSURE TO EPIDURAL ANESTHESIA WAS ASSOCIATED WITH A MARGINALLY LOWER RISK OF ASTHMA (ODDS RATIO = 0.88, 95% CONFIDENCE INTERVAL = 0.76-1.01) FOR EACH 1-H INCREASE IN EXPOSURE TO EPIDURAL ANESTHESIA. OF THE 20 CPGS IN THE NHB POPULATION SHOWING THE STRONGEST MEDIATION EFFECT, 50% DEMONSTRATED AN AVERAGE MEDIATION PROPORTION OF 52%, WITH DIRECTIONAL CONSISTENCY OF DIRECT AND INDIRECT EFFECTS. THESE TOP 20 CPGS MAPPED TO 21 GENES ENRICHED FOR PATHWAYS ENGAGED IN ANTIGEN PROCESSING, ANTIGEN PRESENTATION, PROTEIN UBIQUITINATION AND REGULATORY NETWORKS RELATED TO THE MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) CLASS I COMPLEX AND NUCLEAR FACTOR KAPPA-B (NFKB) COMPLEX. OUR FINDINGS SUGGEST THAT DNA METHYLATION IN IMMUNE-RELATED PATHWAYS CONTRIBUTES TO THE EFFECTS OF THE DURATION OF EXPOSURE TO EPIDURAL ANESTHESIA ON CHILDHOOD ASTHMA RISK IN NHB OFFSPRING. 2023 8 3070 30 GENOME-WIDE DNA METHYLATION PROFILING IN CD8 T-CELLS AND GAMMA DELTA T-CELLS OF ASIAN INDIAN PATIENTS WITH TAKAYASU ARTERITIS. BACKGROUND: TAKAYASU'S ARTERITIS (TA) IS A CHRONIC INFLAMMATORY DISEASE THAT AFFECTS AORTA AND ITS MAIN BRANCHES AT THEIR ORIGIN. GENETIC, PATHOLOGICAL AND FUNCTIONAL STUDIES HAVE SHOWN THAT CD8 AND GAMMA DELTA (GAMMA/DELTA) T-LYMPHOCYTES ARE INVOLVED IN INFLAMMATORY PROCESSES IN AFFECTED REGIONS OF ARTERIES CAUSING VASCULAR DAMAGE. THE MOLECULAR FUNCTION OF THESE LYMPHOCYTES REMAINS UNCLEAR AND CURRENTLY NO EPIGENETIC STUDIES ARE AVAILABLE IN TA. WE PRIMARILY PERFORMED GENOME WIDE METHYLATION ANALYSIS IN CD8 T CELLS AND GAMMADELTA T CELLS OF PATIENTS WITH TA AND COMPARED WITH HEALTHY CONTROLS. METHODS: WE RECRUITED 12 SUBJECTS IN EACH GROUP NAMELY TA PATIENT AND HEALTHY CONTROLS. BLOOD SAMPLES WERE COLLECTED AFTER OBTAINING INFORMED WRITTEN CONSENT. CD8 T CELLS AND GAMMADELTA T CELLS WERE SEPARATED FROM WHOLE BLOOD. DNA EXTRACTED FROM THESE CELLS AND WERE SUBJECTED TO BISULFITE TREATMENT. FINALLY, BISULFITE TREATED DNA WAS LOADED IN INFINIUM METHYLATION EPIC ARRAY. BIOINFORMATICS ANALYSIS WAS USED TO IDENTIFY DIFFERENTIAL METHYLATION REGIONS WHICH WERE THEN MAPPED TO GENES. RESULTS: INTERLEUKIN (IL)-32 AND LYMPHOTOXIN-A WERE GENES SIGNIFICANTLY HYPOMETHYLATED IN CD8 T-CELLS. ANTI-INFLAMMATORY CYTOKINE GENES, IL-10, IL-1RN AND IL-27 WERE HYPOMETHYLATED IN GAMMADELTA T CELLS OF TA PATIENTS AS COMPARED TO HEALTHY CONTROLS. GENE ENRICHMENT ANALYSIS USING GENE ONTOLOGY (GO) DATABASE AND KYOTO ENCYCLOPAEDIA OF GENES AND GENOMES (KEGG) IDENTIFIED THAT GENES INVOLVED IN T-CELL RECEPTOR SIGNALLING PATHWAYS WERE HYPOMETHYLATED IN CD8 T-CELLS AND HYPERMETHYLATED IN GAMMADELTA T CELLS OF TA PATIENTS. CONCLUSION: CD8 T-CELLS MIGHT PLAY A MAJOR ROLE IN IMMUNOPATHOGENESIS OF INFLAMMATION IN TA, WHEREAS GAMMADELTA T CELLS MAY PLAY A REGULATORY ROLE. 2022 9 6194 33 THE IMPACT OF PROTEIN ACETYLATION/DEACETYLATION ON SYSTEMIC LUPUS ERYTHEMATOSUS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC INFLAMMATORY AUTOIMMUNE DISEASE IN WHICH THE BODY'S IMMUNE SYSTEM MISTAKENLY ATTACKS HEALTHY CELLS. ALTHOUGH THE EXACT CAUSE OF SLE HAS NOT BEEN IDENTIFIED, IT IS CLEAR THAT BOTH GENETICS AND ENVIRONMENTAL FACTORS TRIGGER THE DISEASE. IDENTICAL TWINS HAVE A 24% CHANCE OF GETTING LUPUS DISEASE IF THE OTHER ONE IS AFFECTED. INTERNAL FACTORS SUCH AS FEMALE GENDER AND SEX HORMONES, THE MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) LOCUS AND OTHER GENETIC POLYMORPHISMS HAVE BEEN SHOWN TO AFFECT SLE, AS WELL AS EXTERNAL, ENVIRONMENTAL INFLUENCES SUCH AS SUNLIGHT EXPOSURE, SMOKING, VITAMIN D DEFICIENCY, AND CERTAIN INFECTIONS. SEVERAL STUDIES HAVE REPORTED AND PROPOSED MULTIPLE ASSOCIATIONS BETWEEN THE ALTERATION OF THE EPIGENOME AND THE PATHOGENESIS OF AUTOIMMUNE DISEASE. EPIGENETIC FACTORS CONTRIBUTING TO SLE INCLUDE MICRORNAS, DNA METHYLATION STATUS, AND THE ACETYLATION/DEACETYLATION OF HISTONE PROTEINS. ADDITIONALLY, THE ACETYLATION OF NON-HISTONE PROTEINS CAN ALSO INFLUENCE CELLULAR FUNCTION. A BETTER UNDERSTANDING OF NON-GENOMIC FACTORS THAT REGULATE SLE WILL PROVIDE INSIGHT INTO THE MECHANISMS THAT INITIATE AND FACILITATE DISEASE AND ALSO CONTRIBUTE TO THE DEVELOPMENT OF NOVEL THERAPEUTICS THAT CAN SPECIFICALLY TARGET PATHOGENIC MOLECULAR PATHWAYS. 2018 10 2973 44 GENETIC AND EPIGENETIC STUDIES OF ATOPIC DERMATITIS. BACKGROUND: ATOPIC DERMATITIS (AD) IS A CHRONIC INFLAMMATORY DISEASE CAUSED BY THE COMPLEX INTERACTION OF GENETIC, IMMUNE AND ENVIRONMENTAL FACTORS. THERE HAVE MANY RECENT DISCOVERIES INVOLVING THE GENETIC AND EPIGENETIC STUDIES OF AD. METHODS: A RETROSPECTIVE PUBMED SEARCH WAS CARRIED OUT FROM JUNE 2009 TO JUNE 2016 USING THE TERMS "ATOPIC DERMATITIS", "ASSOCIATION", "ECZEMA", "GENE", "POLYMORPHISM", "MUTATION", "VARIANT", "GENOME WIDE ASSOCIATION STUDY", "MICROARRAY" "GENE PROFILING", "RNA SEQUENCING", "EPIGENETICS" AND "MICRORNA". A TOTAL OF 132 PUBLICATIONS IN ENGLISH WERE IDENTIFIED. RESULTS: TO ELUCIDATE THE GENETIC FACTORS FOR AD PATHOGENESIS, CANDIDATE GENE ASSOCIATION STUDIES, GENOME-WIDE ASSOCIATION STUDIES (GWAS) AND TRANSCRIPTOMIC PROFILING ASSAYS HAVE BEEN PERFORMED IN THIS PERIOD. EPIGENETIC MECHANISMS FOR AD DEVELOPMENT, INCLUDING GENOMIC DNA MODIFICATION AND MICRORNA POSTTRANSCRIPTIONAL REGULATION, HAVE BEEN EXPLORED. TO DATE, CANDIDATE GENE ASSOCIATION STUDIES INDICATE THAT FILAGGRIN (FLG) NULL GENE MUTATIONS ARE THE MOST SIGNIFICANT KNOWN RISK FACTOR FOR AD, AND GENES IN THE TYPE 2 T HELPER LYMPHOCYTE (TH2) SIGNALING PATHWAYS ARE THE SECOND REPLICATED GENETIC RISK FACTOR FOR AD. GWAS STUDIES IDENTIFIED 34 RISK LOCI FOR AD, THESE LOCI ALSO SUGGEST THAT GENES IN IMMUNE RESPONSES AND EPIDERMAL SKIN BARRIER FUNCTIONS ARE ASSOCIATED WITH AD. ADDITIONALLY, GENE PROFILING ASSAYS DEMONSTRATED AD IS ASSOCIATED WITH DECREASED GENE EXPRESSION OF EPIDERMAL DIFFERENTIATION COMPLEX GENES AND ELEVATED TH2 AND TH17 GENES. HYPOMETHYLATION OF TSLP AND FCER1G IN AD WERE REPORTED; AND MIR-155, WHICH TARGET THE IMMUNE SUPPRESSOR CTLA-4, WAS FOUND TO BE SIGNIFICANTLY OVER-EXPRESSED IN INFILTRATING T CELLS IN AD SKIN LESIONS. CONCLUSIONS: THE RESULTS SUGGEST THAT TWO MAJOR BIOLOGIC PATHWAYS ARE RESPONSIBLE FOR AD ETIOLOGY: SKIN EPITHELIAL FUNCTION AND INNATE/ADAPTIVE IMMUNE RESPONSES. THE DYSFUNCTIONAL EPIDERMAL BARRIER AND IMMUNE RESPONSES RECIPROCALLY AFFECT EACH OTHER, AND THEREBY DRIVE DEVELOPMENT OF AD. 2016 11 6608 37 TYPE I INTERFERONS AS KEY PLAYERS IN PANCREATIC BETA-CELL DYSFUNCTION IN TYPE 1 DIABETES. TYPE 1 DIABETES (T1D) IS A CHRONIC AUTOIMMUNE DISEASE CHARACTERIZED BY PANCREATIC ISLET INFLAMMATION (INSULITIS) AND SPECIFIC PANCREATIC BETA-CELL DESTRUCTION BY AN IMMUNE ATTACK. ALTHOUGH THE PRECISE UNDERLYING MECHANISMS LEADING TO THE AUTOIMMUNE ASSAULT REMAIN POORLY UNDERSTOOD, IT IS WELL ACCEPTED THAT INSULITIS TAKES PLACE IN THE CONTEXT OF A CONFLICTING DIALOGUE BETWEEN PANCREATIC BETA-CELLS AND THE IMMUNE CELLS. MOREOVER, BOTH HOST GENETIC BACKGROUND (I.E., CANDIDATE GENES) AND ENVIRONMENTAL FACTORS (E.G., VIRAL INFECTIONS) CONTRIBUTE TO THIS INADEQUATE DIALOGUE. ACCUMULATING EVIDENCE INDICATES THAT TYPE I INTERFERONS (IFNS), CYTOKINES THAT ARE CRUCIAL FOR BOTH INNATE AND ADAPTIVE IMMUNE RESPONSES, ACT AS KEY LINKS BETWEEN ENVIRONMENTAL AND GENETIC RISK FACTORS IN THE DEVELOPMENT OF T1D. THIS CHAPTER SUMMARIZES SOME RELEVANT PATHWAYS INVOLVED IN BETA-CELL DYSFUNCTION AND DEATH, AND BRIEFLY REVIEWS HOW ENTEROVIRAL INFECTIONS AND GENETIC SUSCEPTIBILITY CAN IMPACT INSULITIS. MOREOVER, WE PRESENT THE CURRENT EVIDENCE SHOWING THAT, IN BETA-CELLS, TYPE I IFN SIGNALING PATHWAY ACTIVATION LEADS TO SEVERAL OUTCOMES, SUCH AS LONG-LASTING MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) CLASS I HYPEREXPRESSION, ENDOPLASMIC RETICULUM (ER) STRESS, EPIGENETIC CHANGES, AND INDUCTION OF POSTTRANSCRIPTIONAL AS WELL AS POSTTRANSLATIONAL MODIFICATIONS. MHC CLASS I OVEREXPRESSION, WHEN COMBINED WITH ER STRESS AND POSTTRANSCRIPTIONAL/POSTTRANSLATIONAL MODIFICATIONS, MIGHT LEAD TO SUSTAINED NEOANTIGEN PRESENTATION TO IMMUNE SYSTEM AND BETA-CELL APOPTOSIS. THIS KNOWLEDGE SUPPORTS THE CONCEPT THAT TYPE I IFNS ARE IMPLICATED IN THE EARLY STAGES OF T1D PATHOGENESIS. FINALLY, WE HIGHLIGHT THE PROMISING THERAPEUTIC AVENUES FOR T1D TREATMENT DIRECTED AT TYPE I IFN SIGNALING PATHWAY. 2021 12 5393 39 REDUCED CHROMATIN ACCESSIBILITY TO CD4 T CELL SUPER-ENHANCERS ENCOMPASSING SUSCEPTIBILITY LOCI OF RHEUMATOID ARTHRITIS. BACKGROUND: RHEUMATOID ARTHRITIS (RA) IS AN INFLAMMATORY DISEASE THAT MANIFESTS AS A PRECLINICAL STAGE OF SYSTEMIC AUTOIMMUNITY FOLLOWED BY CHRONIC PROGRESSIVE SYNOVITIS. DISEASE-ASSOCIATED GENETIC SNP VARIANTS PREDOMINANTLY MAP TO NON-CODING, REGULATORY REGIONS OF FUNCTIONAL IMPORTANCE IN CD4 T CELLS, IMPLICATING THESE CELLS AS KEY REGULATORS. A BETTER UNDERSTANDING OF THE EPIGENOME OF CD4 T CELLS HOLDS THE PROMISE OF PROVIDING INFORMATION ON THE INTERACTION BETWEEN GENETIC SUSCEPTIBILITY AND EXOGENOUS FACTORS. METHODS: WE MAPPED REGIONS OF CHROMATIN ACCESSIBILITY USING ATAC-SEQ IN PERIPHERAL CD4 T CELL SUBSETS OF PATIENTS WITH RA (N=18) AND COMPARED THEM TO T CELLS FROM PATIENTS WITH PSORIATIC ARTHRITIS (N=11) AND AGE-MATCHED HEALTHY CONTROLS (N=10). TRANSCRIPTS OF SELECTED GENES WERE QUANTIFIED USING QPCR. FINDINGS: RA-ASSOCIATED EPIGENETIC SIGNATURES WERE IDENTIFIED THAT IN PART OVERLAPPED BETWEEN CENTRAL AND EFFECTOR MEMORY CD4 T CELLS AND THAT WERE TO A LESSER EXTENT ALREADY PRESENT IN NAIVE CELLS. SITES MORE ACCESSIBLE IN RA WERE HIGHLY ENRICHED FOR THE MOTIF OF THE TRANSCRIPTION FACTOR (TF) CTCF SUGGESTING DIFFERENCES IN THE THREE-DIMENSIONAL CHROMATIN STRUCTURE. UNEXPECTEDLY, SITES WITH REDUCED CHROMATIN ACCESSIBILITY WERE ENRICHED FOR MOTIFS OF TFS PERTINENT FOR T CELL FUNCTION. MOST STRIKINGLY, SUPER-ENHANCERS ENCOMPASSING RA-ASSOCIATED SNPS WERE LESS ACCESSIBLE. ANALYSIS OF SELECTED TRANSCRIPTS AND PUBLISHED DNA METHYLATION PATTERNS WERE CONSISTENT WITH THIS FINDING. THE PREFERENTIAL LOSS IN ACCESSIBILITY AT THESE SUPER-ENHANCERS WAS SEEN IN PATIENTS WITH HIGH AND LOW DISEASE ACTIVITY AND ON A VARIETY OF IMMUNOSUPPRESSIVE TREATMENT MODALITIES. INTERPRETATION: DISEASE-ASSOCIATED GENES ARE EPIGENETICALLY LESS POISED TO RESPOND IN CD4 T CELLS FROM PATIENTS WITH ESTABLISHED RA. FUNDING: THIS WORK WAS SUPPORTED BY I01 BX001669 FROM THE VETERANS ADMINISTRATION. 2022 13 3857 37 ISCHEMIA- REPERFUSION INJURY AND ITS INFLUENCE ON THE EPIGENETIC MODIFICATION OF THE DONOR KIDNEY GENOME. BACKGROUND: IN CLINICAL TRANSPLANTATION, ISCHEMIA-REPERFUSION INJURY (I/RI) CAUSES DAMAGE TO DNA. WE HYPOTHESIZE THAT ONE FORM OF DAMAGE IS THE DEMETHYLATION OF METHYLATED CYTOSINES IN THE DONOR GENOME CAUSED BY THE OXIDATIVE ENVIRONMENT CREATED FIRST BY ISCHEMIA, AND SUBSEQUENTLY BY REPERFUSION ON TRANSPLANTATION. THIS STUDY CONTRIBUTES TO THE UNDERSTANDING OF HOW THE SHORT-LIVED AND TRANSIENT ISCHEMIC INSULT MAY INFLUENCE CHRONIC PATHOLOGICAL CHANGES THAT OCCUR IN CLINICAL TRANSPLANTATION IN THE LONG TERM. METHODS: A MODEL OF I/RI AND CHRONIC REJECTION; FISHER TO FISHER KIDNEY TRANSPLANT RENDERED COLD-ISCHEMIC FOR 4 HR BEFORE TRANSPLANTATION, TO INDUCE ANTIGEN-INDEPENDENT CHRONIC NEPHROPATHY OVER A 6-MONTH PERIOD, WAS USED. TISSUE WAS ASSESSED BY HISTOPATHOLOGY AND METHYLATION BY PYROSEQUENCING ANALYSIS. RESULTS: AN EPIGENETIC MAP OF THE RAT RENAL C3 PROMOTER WAS PRODUCED, WHICH IDENTIFIED METHYLATED CYTOSINE PHOSPHO GUANINE (CPG) SITES COINCIDENT TO CYTOKINE RESPONSE ELEMENTS AND NUCLEAR FACTOR KAPPA-LIGHT-CHAIN-ENHANCER OF ACTIVATED B CELLS (NF-KAPPAB) BINDING SITES. PYROSEQUENCING ANALYSIS SHOWED THAT THE TISSUE THAT HAD UNDERGONE 4 HR ISCHEMIA AND REPERFUSION DEVELOPED ABERRANT DEMETHYLATION OF CYTOSINES IN PUTATIVE REGULATORY SITES WITHIN THE C3 PROMOTER. CONCLUSION: THESE FINDINGS MAY DESCRIBE A NEWLY RECOGNIZED PHENOMENA IN THE FIELD OF TRANSPLANTATION. ABERRANT DEMETHYLATION HAS LONG BEEN LINKED TO THE DEVELOPMENT OF TUMORS, AND OUR DATA SUGGEST A SIMILAR MECHANISM OF GENE DYSREGULATION THAT MAY BE INITIATED BY I/RI WITH ACUTE AND CHRONIC EFFECTS. THESE DATA MAY CONTRIBUTE TO A FURTHER UNDERSTANDING OF HOW THE SHORT LIVED AND TRANSIENT ISCHEMIC INSULT INFLUENCES CHRONIC PATHOLOGICAL CHANGES THAT OCCUR EVEN IN THE ABSENCE OF MAJOR HISTOCOMPATIBILITY COMPLEX DISPARITY IN TRANSPLANTATION. 2008 14 5760 31 SOLUBLE URIC ACID PRIMES TLR-INDUCED PROINFLAMMATORY CYTOKINE PRODUCTION BY HUMAN PRIMARY CELLS VIA INHIBITION OF IL-1RA. OBJECTIVES: THE STUDY OF THE PROINFLAMMATORY ROLE OF URIC ACID HAS FOCUSED ON THE EFFECTS OF ITS CRYSTALS OF MONOSODIUM URATE (MSU). HOWEVER, LITTLE IS KNOWN WHETHER URIC ACID ITSELF CAN DIRECTLY HAVE PROINFLAMMATORY EFFECTS. IN THIS STUDY, WE INVESTIGATE THE PRIMING EFFECTS OF URIC ACID EXPOSURE ON THE CYTOKINE PRODUCTION OF PRIMARY HUMAN CELLS UPON STIMULATION WITH GOUT-RELATED STIMULI. METHODS: PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) WERE HARVESTED FROM PATIENTS WITH GOUT AND HEALTHY VOLUNTEERS. CELLS WERE PRETREATED WITH OR WITHOUT URIC ACID IN SOLUBLE FORM FOR 24 H AND THEN STIMULATED FOR 24 H WITH TOLL-LIKE RECEPTOR (TLR)2 OR TLR4 LIGANDS IN THE PRESENCE OR ABSENCE OF MSU CRYSTALS. CYTOKINE PRODUCTION WAS MEASURED BY ELISA; MRNA LEVELS WERE ASSESSED USING QPCR. RESULTS: THE PRODUCTION OF INTERLEUKIN (IL)-1BETA AND IL-6 WAS HIGHER IN PATIENTS COMPARED WITH CONTROLS AND THIS CORRELATED WITH SERUM URATE LEVELS. PROINFLAMMATORY CYTOKINE PRODUCTION WAS SIGNIFICANTLY POTENTIATED WHEN CELLS FROM HEALTHY SUBJECTS WERE PRETREATED WITH URIC ACID. SURPRISINGLY, THIS WAS ASSOCIATED WITH A SIGNIFICANT DOWNREGULATION OF THE ANTI-INFLAMMATORY CYTOKINE IL-1 RECEPTOR ANTAGONIST (IL-1RA). THIS EFFECT WAS SPECIFIC TO STIMULATION BY URIC ACID AND WAS EXERTED AT THE LEVEL OF GENE TRANSCRIPTION. EPIGENETIC REPROGRAMMING AT THE LEVEL OF HISTONE METHYLATION BY URIC ACID WAS INVOLVED IN THIS EFFECT. CONCLUSIONS: IN THIS STUDY WE DEMONSTRATE A MECHANISM THROUGH WHICH HIGH CONCENTRATIONS OF URIC ACID (UP TO 50 MG/DL) INFLUENCE INFLAMMATORY RESPONSES BY FACILITATING IL-1BETA PRODUCTION IN PBMCS. WE SHOW THAT A MECHANISM FOR THE AMPLIFICATION OF IL-1BETA CONSISTS IN THE DOWNREGULATION OF IL-1RA AND THAT THIS EFFECT COULD BE EXERTED VIA EPIGENETIC MECHANISMS SUCH AS HISTONE METHYLATION. HYPERURICAEMIA CAUSES A SHIFT IN THE IL-1BETA/IL-1RA BALANCE PRODUCED BY PBMCS AFTER EXPOSURE TO MSU CRYSTALS AND TLR-MEDIATED STIMULI, AND THIS PHENOMENON IS LIKELY TO REINFORCE THE ENHANCED STATE OF CHRONIC INFLAMMATION. 2016 15 3501 36 IDENTIFICATION OF POTENTIAL BIOMARKERS FOR SYSTEMIC LUPUS ERYTHEMATOSUS BY INTEGRATED ANALYSIS OF GENE EXPRESSION AND METHYLATION DATA. INTRODUCTION: SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A HETEROGENEOUS AND CHRONIC AUTOIMMUNE DISEASE. ABERRANT DNA METHYLATION OCCURS DURING VARIOUS PROCESSES OF SLE DEVELOPMENT REGULATING THE MRNA EXPRESSION OF INTERRELATED GENES. THIS STUDY AIMS TO SCREEN POTENTIAL DNA METHYLATION MARKERS FOR SLE. METHODS: GENE EXPRESSION AND METHYLATION DATASETS WERE DOWNLOADED FROM THE GENE EXPRESSION OMNIBUS (GEO) DATABASE. DIFFERENTIALLY EXPRESSED GENES (DEGS) BETWEEN SLE PATIENTS AND HEALTHY CONTROLS WERE SCREENED USING THE LIMMA R PACKAGE, AND DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AND REGIONS (DMRS) WERE IDENTIFIED USING DMPFINDER AND BUMPHUNTER (MINFI). ADDITIONALLY, THE DNA METHYLATION MARKERS TO DISTINGUISH SLE PATIENTS FROM HEALTHY CONTROLS WERE EXPLORED THROUGH RECEIVER OPERATING CHARACTERISTIC (ROC) CURVES AND LOGISTIC REGRESSION ANALYSES. FINALLY, WE VALIDATED THE RESULTS OF THE BIOINFORMATIC ANALYSIS BY PYROSEQUENCING. RESULTS: IN TOTAL, 91 DEGS, 90,092 DMPS, 15 DMRS, AND 13 DMR-ASSOCIATED GENES WERE IDENTIFIED. THROUGH THE INTEGRATIVE ANALYSIS OF DEG- AND DMR-ASSOCIATED GENES, WE IDENTIFIED FIVE TYPE I INTERFERON (IFN)-RELATED GENES AS KEY EPIGENETIC-DRIVEN GENES IN SLE. GO ENRICHMENT ANALYSIS SHOWED THAT THE FIVE SLE-ASSOCIATED EPIGENETIC-DRIVEN GENES WERE MAINLY ENRICHED IN THE TYPE I IFN SIGNALING PATHWAY INVOLVED IN IMMUNE RESPONSE AND DEFENSE RESPONSE TO VIRUS. MOREOVER, WE IDENTIFIED TWO SLE-SPECIFIC DNA METHYLATION MARKERS, THREE SLE WITHOUT LUPUS NEPHRITIS (SLE-LN(-))-SPECIFIC DNA METHYLATION MARKERS, AND TWO SLE WITH LUPUS NEPHRITIS (SLE-LN(+))-SPECIFIC DNA METHYLATION MARKERS BY STEPWISE LOGISTIC REGRESSION. CONCLUSIONS: OVERALL, OUR STUDY DEMONSTRATES POTENTIAL DNA METHYLATION MARKERS OF SLE, SLE-LN(-), AND SLE-LN(+), WHICH MAY HELP THE DIAGNOSIS, BOOST THE DEVELOPMENT OF NEW EPIGENETIC THERAPY, AND CONTRIBUTE TO INDIVIDUALIZED TREATMENT. KEY POINTS * THIS STUDY IDENTIFIED FIVE TYPE I IFN-RELATED GENES AS KEY EPIGENETIC-DRIVEN GENES IN SLE, WHICH SUPPORT THE IMPORTANCE OF THE TYPE I IFN PATHWAY IN THE PATHOGENESIS OF SLE * WE IDENTIFIED NOVEL DNA METHYLATION BIOMARKERS IN SLE, SLE-LN-, AND SLE-LN+ BY A COMPREHENSIVE ANALYSIS OF BIOINFORMATICS METHODS AND EXECUTED EXPERIMENTAL VALIDATION, AND BINARY LOGISTIC REGRESSION ANALYSIS SHOWED THAT THEY HAVE EXCELLENT POTENTIAL * THESE RESULTS MAY PROVIDE NEW INSIGHTS INTO THE BIOLOGICAL MECHANISMS OF SLE, AND IDENTIFY RELIABLE BIOMARKERS FOR SLE, SLE-LN-, AND SLE-LN+, WHICH MAY CONTRIBUTE TO DIAGNOSIS AND INDIVIDUALIZED TREATMENT. 2023 16 42 39 A COMPREHENSIVE GENOME-WIDE PROFILING COMPARISON BETWEEN HBV AND HCV INFECTED HEPATOCELLULAR CARCINOMA. BACKGROUND: HEPATOCELLULAR CARCINOMA (HCC) IS ONE OF THE MOST COMMON CANCERS WORLDWIDE, ESPECIALLY IN EAST ASIA. EVEN WITH THE PROGRESS IN THERAPY, 5-YEAR SURVIVAL RATES REMAIN UNSATISFIED. CHRONIC INFECTION WITH THE HEPATITIS B VIRUS (HBV) OR HEPATITIS C VIRUS (HCV) HAS BEEN EPIDEMIOLOGICALLY ASSOCIATED WITH HCC AND IS THE MAJOR ETIOLOGY IN THE EAST ASIAN POPULATION. THE DETAILED MECHANISM, ESPECIALLY THE CHANGES OF DNA METHYLATION AND GENE EXPRESSION BETWEEN THE TWO TYPES OF VIRUS-RELATED HCC, AND THEIR CONTRIBUTIONS TO THE HCC DEVELOPMENT, METASTASIS, AND RECURRENCE REMAIN LARGELY UNKNOWN. METHODS: IN THIS INTEGRATED ANALYSIS, WE CHARACTERIZED GENOME-SCALE PROFILES OF HBV AND HCV INFECTED HCC BY COMPARING THEIR GENE EXPRESSION PATTERN, METHYLATION PROFILES, AND COPY NUMBER VARIATIONS FROM THE PUBLICLY ACCESSIBLE DATA OF THE CANCER GENOME ATLAS PROGRAM (TCGA). RESULTS: THE HLA-A, STAT1, AND OAS2 GENES WERE HIGHLY ENRICHED AND UP-REGULATED DISCOVERED IN THE HCV-INFECTED HCC. HYPOMETHYLATION BUT NOT COPY NUMBER VARIATIONS MIGHT BE THE MAJOR FACTOR FOR THE UP-REGULATION OF THESE IMMUNE-RELATED GENES IN HCV-INFECTED HCC. CONCLUSIONS: THE RESULTS INDICATED THE DIFFERENT EPIGENETIC CHANGES OF HBV/HCV RELATED HEPATOCARCINOGENESIS. THE TOP UP-REGULATED GENES IN HCV GROUP WERE SIGNIFICANTLY CLUSTERED IN THE IMMUNE-RELATED AND DEFENSE RESPONSE PATHWAYS. THESE FINDINGS WILL HELP US TO UNDERSTAND THE PATHOGENESIS OF HBV/HCV ASSOCIATED HEPATOCELLULAR CARCINOMA. 2019 17 2765 44 EXPRESSION, EPIGENETIC REGULATION, AND HUMORAL IMMUNOGENICITY OF CANCER-TESTIS ANTIGENS IN CHRONIC MYELOID LEUKEMIA. OBJECTIVE: CANCER-TESTIS (CT) ANTIGENS REPRESENT ATTRACTIVE TARGETS FOR TUMOR IMMUNOTHERAPY BASED ON THEIR TUMOR-RESTRICTED EXPRESSION AND IMMUNOGENICITY. HOWEVER, A BROAD PICTURE OF THE EXPRESSION OF CT ANTIGENS AND ASSOCIATED HUMORAL IMMUNE RESPONSES IN CHRONIC MYELOID LEUKEMIA (CML) IS STILL MISSING. METHODS: WE SCREENED CML CELL LINES AND BONE MARROW (BM) SAMPLES FROM HEALTHY DONORS BY RT-PCR FOR THE EXPRESSION OF 31 CT ANTIGENS BEFORE AND AFTER TREATMENT WITH EPIGENETIC AGENTS. EXPRESSION OF TUMOR-RESTRICTED ANTIGENS WAS FURTHER EXAMINED IN 60 CML PATIENTS AND HUMORAL IMMUNE RESPONSES AGAINST 15 CT ANTIGENS WERE SCREENED BY ELISA. RESULTS: IN UNTREATED CELL LINES WE DETECTED THE EXPRESSION OF 17 CT ANTIGENS THAT WERE ABSENT FROM NORMAL BM. EXPRESSION OF MOST ANTIGENS INCREASED FOLLOWING DEMETHYLATING TREATMENT WITH 5'-AZA-2'-DEOXYCYTIDINE. IN THESE SAMPLES, ONLY PRAME WAS REPEATEDLY DETECTED AND EXPRESSION CORRELATED WITH SEVERAL CLINICOPATHOLOGICAL PARAMETERS AND DECREASED OVERALL SURVIVAL. WE FURTHER SHOW THAT A LOWER FREQUENCY OF PRAME-POSITIVE SAMPLES DURING IMATINIB TREATMENT WAS NOT CAUSED BY GENE-SPECIFIC DOWNREGULATION. ANALYZING THE PATIENTS' ANTIBODY RESPONSES WE FOUND THAT THE VAST MAJORITY OF PATIENTS LACKED SPONTANEOUS IMMUNITY AGAINST CT ANTIGENS INCLUDING PRAME. CONCLUSIONS: CT ANTIGEN EXPRESSION CAN BE INCREASED BY THE APPLICATION OF EPIGENETIC AGENTS AND THE EXPRESSION OF PRAME CORRELATES WITH CLINICOPATHOLOGICAL PARAMETERS AND OVERALL SURVIVAL IN PATIENTS WITH CML, BUT DOES NOT LEAD TO HUMORAL IMMUNE RESPONSES. PRAME-SPECIFIC IMMUNOTHERAPY MIGHT REPRESENT A PROMISING APPROACH FOR THE ERADICATION OF RESIDUAL THERAPY-RESISTANT LEUKEMIC CELLS DUE TO ITS FREQUENT EXPRESSION AND STABILITY UNDER IMATINIB TREATMENT. 2010 18 6275 50 THE PATHOGENESIS OF SYSTEMIC LUPUS ERYTHEMATOSUS: HARNESSING BIG DATA TO UNDERSTAND THE MOLECULAR BASIS OF LUPUS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC, SYSTEMIC AUTOIMMUNE DISEASE THAT CAUSES DAMAGE TO MULTIPLE ORGAN SYSTEMS. DESPITE DECADES OF RESEARCH AND AVAILABLE MURINE MODELS THAT CAPTURE SOME ASPECTS OF THE HUMAN DISEASE, NEW TREATMENTS FOR SLE LAG BEHIND OTHER AUTOIMMUNE DISEASES SUCH AS RHEUMATOID ARTHRITIS AND CROHN'S DISEASE. BIG DATA GENOMIC ASSAYS HAVE TRANSFORMED OUR UNDERSTANDING OF SLE BY PROVIDING IMPORTANT INSIGHTS INTO THE MOLECULAR HETEROGENEITY OF THIS MULTIGENIC DISEASE. GENE WIDE ASSOCIATION STUDIES HAVE DEMONSTRATED MORE THAN 100 RISK LOCI, SUPPORTING A MODEL OF MULTIPLE GENETIC HITS INCREASING SLE RISK IN A NON-LINEAR FASHION, AND PROVIDING EVIDENCE OF ANCESTRAL DIVERSITY IN SUSCEPTIBILITY LOCI. EPIGENETIC STUDIES TO DETERMINE THE ROLE OF METHYLATION, ACETYLATION AND NON-CODING RNAS HAVE PROVIDED NEW UNDERSTANDING OF THE MODULATION OF GENE EXPRESSION IN SLE PATIENTS AND IDENTIFIED NEW DRUG TARGETS AND BIOMARKERS FOR SLE. GENE EXPRESSION PROFILING HAS LED TO A GREATER UNDERSTANDING OF THE ROLE OF MYELOID CELLS IN THE PATHOGENESIS OF SLE, CONFIRMED ROLES FOR T AND B CELLS IN SLE, PROMOTED CLINICAL TRIALS BASED ON THE PROMINENT INTERFERON SIGNATURE FOUND IN SLE PATIENTS, AND IDENTIFIED CANDIDATE BIOMARKERS AND CELLULAR SIGNATURES TO FURTHER DRUG DEVELOPMENT AND DRUG REPURPOSING. GENE EXPRESSION STUDIES ARE ADVANCING OUR UNDERSTANDING OF THE UNDERLYING MOLECULAR HETEROGENEITY IN SLE AND PROVIDING HOPE THAT PATIENT STRATIFICATION WILL EXPEDITE NEW THERAPIES BASED ON PERSONAL MOLECULAR SIGNATURES. ALTHOUGH BIG DATA ANALYSES PRESENT UNIQUE INTERPRETATION CHALLENGES, BOTH COMPUTATIONALLY AND BIOLOGICALLY, ADVANCES IN MACHINE LEARNING APPLICATIONS MAY FACILITATE THE ABILITY TO PREDICT CHANGES IN SLE DISEASE ACTIVITY AND OPTIMIZE THERAPEUTIC STRATEGIES. 2020 19 938 39 CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) RISK IS MEDIATED BY MULTIPLE ENHANCER VARIANTS WITHIN CLL RISK LOCI. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS THE MOST COMMON ADULT LEUKEMIA IN WESTERN COUNTRIES. IT HAS A STRONG GENETIC BASIS, SHOWING A ~ 8-FOLD INCREASED RISK OF CLL IN FIRST-DEGREE RELATIVES. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED 41 RISK VARIANTS ACROSS 41 LOCI. HOWEVER, FOR A MAJORITY OF THE LOCI, THE FUNCTIONAL VARIANTS AND THE MECHANISMS UNDERLYING THEIR CAUSAL ROLES REMAIN UNDEFINED. HERE, WE EXAMINED THE GENETIC AND EPIGENETIC FEATURES ASSOCIATED WITH 12 INDEX VARIANTS, ALONG WITH ANY CORRELATED (R2 >/= 0.5) VARIANTS, AT THE CLL RISK LOCI LOCATED OUTSIDE OF GENE PROMOTERS. BASED ON PUBLICLY AVAILABLE CHIP-SEQ AND CHROMATIN ACCESSIBILITY DATA AS WELL AS OUR OWN CHIP-SEQ DATA FROM CLL PATIENTS, WE IDENTIFIED SIX CANDIDATE FUNCTIONAL VARIANTS AT SIX LOCI AND AT LEAST TWO CANDIDATE FUNCTIONAL VARIANTS AT EACH OF THE REMAINING SIX LOCI. THE FUNCTIONAL VARIANTS ARE PREDOMINANTLY LOCATED WITHIN ENHANCERS OR SUPER-ENHANCERS, INCLUDING BI-DIRECTIONALLY TRANSCRIBED ENHANCERS, WHICH ARE OFTEN RESTRICTED TO IMMUNE CELL TYPES. FURTHERMORE, WE FOUND THAT, AT 78% OF THE FUNCTIONAL VARIANTS, THE ALTERNATIVE ALLELES ALTERED THE TRANSCRIPTION FACTOR BINDING MOTIFS OR HISTONE MODIFICATIONS, INDICATING THE INVOLVEMENT OF THESE VARIANTS IN THE CHANGE OF LOCAL CHROMATIN STATE. FINALLY, THE ENHANCERS CARRYING FUNCTIONAL VARIANTS PHYSICALLY INTERACTED WITH GENES ENRICHED IN THE TYPE I INTERFERON SIGNALING PATHWAY, APOPTOSIS, OR TP53 NETWORK THAT ARE KNOWN TO PLAY KEY ROLES IN CLL. THESE RESULTS SUPPORT THE REGULATORY ROLES FOR INHERITED NONCODING VARIANTS IN THE PATHOGENESIS OF CLL. 2020 20 1571 46 DNA METHYLATION PATTERNS IN CD8(+) T CELLS DISCERN PSORIASIS FROM PSORIATIC ARTHRITIS AND CORRELATE WITH CUTANEOUS DISEASE ACTIVITY. BACKGROUND: PSORIASIS IS A T CELL-MEDIATED CHRONIC AUTOIMMUNE/INFLAMMATORY DISEASE. WHILE SOME PATIENTS EXPERIENCE DISEASE LIMITED TO THE SKIN (SKIN PSORIASIS), OTHERS DEVELOP JOINT INVOLVEMENT (PSORIATIC ARTHRITIS; PSA). IN THE ABSENCE OF DISEASE- AND/OR OUTCOME-SPECIFIC BIOMARKERS, AND AS ARTHRITIS CAN PRECEDE SKIN MANIFESTATIONS, DIAGNOSTIC AND THERAPEUTIC DELAYS ARE COMMON AND CONTRIBUTE TO DISEASE BURDEN AND DAMAGE ACCRUAL. OBJECTIVE: ALTERED EPIGENETIC MARKS, INCLUDING DNA METHYLATION, CONTRIBUTE TO EFFECTOR T CELL PHENOTYPES AND ALTERED CYTOKINE EXPRESSION IN AUTOIMMUNE/INFLAMMATORY DISEASES. THIS PROJECT AIMED AT THE IDENTIFICATION OF DISEASE-/OUTCOME-SPECIFIC DNA METHYLATION SIGNATURES IN CD8(+) T CELLS FROM PATIENTS WITH PSORIASIS AND PSA AS COMPARED TO HEALTHY CONTROLS. METHOD: PERIPHERAL BLOOD CD8(+) T CELLS FROM NINE HEALTHY CONTROLS, 10 PSORIASIS, AND SEVEN PSA PATIENTS WERE COLLECTED TO ANALYZE DNA METHYLATION MARKS USING ILLUMINA HUMAN METHYLATION EPIC BEADCHIPS (>850,000 CPGS PER SAMPLE). BIOINFORMATIC ANALYSIS WAS PERFORMED USING R (MINFI, LIMMA, CHAMP, AND DMRCATE PACKAGES). RESULTS: DNA METHYLATION PROFILES IN CD8(+) T CELLS DIFFERENTIATE HEALTHY CONTROLS FROM PSORIASIS PATIENTS [397 DIFFERENTIALLY METHYLATED POSITIONS (DMPS); 9 DIFFERENTIALLY METHYLATED REGIONS (DMRS) WHEN >/=CPGS PER DMR WERE CONSIDERED; 2 DMRS FOR >/=10 CPGS]. FURTHERMORE, PATIENTS WITH SKIN PSORIASIS CAN BE DISCRIMINATED FROM PSA PATIENTS [1,861 DMPS, 20 DMRS (>/=5 CPGS PER REGION), 4 DMRS (>/=10 CPGS PER REGION)]. GENE ONTOLOGY (GO) ANALYSES CONSIDERING GENES WITH >/=1 DMP IN THEIR PROMOTER DELIVERED METHYLATION DEFECTS IN SKIN PSORIASIS AND PSA PRIMARILY AFFECTING THE BMP SIGNALING PATHWAY AND ENDOPEPTIDASE REGULATOR ACTIVITY, RESPECTIVELY. GO ANALYSIS OF GENES ASSOCIATED WITH DMRS BETWEEN SKIN PSORIASIS AND PSA DEMONSTRATED AN ENRICHMENT OF GABAERGIC NEURON AND CORTEX NEURON DEVELOPMENT PATHWAYS. TREATMENT WITH CYTOKINE BLOCKERS ASSOCIATED WITH DNA METHYLATION CHANGES [2,372 DMPS; 1,907 DMPS WITHIN PROMOTERS, 7 DMRS (>/=5 CPG PER REGIONS)] AFFECTING TRANSFORMING GROWTH FACTOR BETA RECEPTOR AND TRANSMEMBRANE RECEPTOR PROTEIN SERINE/THREONINE KINASE SIGNALING PATHWAYS. LASTLY, A METHYLATION SCORE INCLUDING TNF AND IL-17 PATHWAY ASSOCIATED DMPS INVERSE CORRELATES WITH SKIN DISEASE ACTIVITY SCORES (PASI). CONCLUSION: PATIENTS WITH SKIN PSORIASIS EXHIBIT DNA METHYLATION PATTERNS IN CD8(+) T CELLS THAT ALLOW DIFFERENTIATION FROM PSA PATIENTS AND HEALTHY INDIVIDUALS, AND REFLECT CLINICAL ACTIVITY OF SKIN DISEASE. THUS, DNA METHYLATION PROFILING PROMISES POTENTIAL AS DIAGNOSTIC AND PROGNOSTIC TOOL TO BE USED FOR MOLECULAR PATIENT STRATIFICATION TOWARD INDIVIDUALIZED TREATMENT. 2021